I used a lot of settings with this scipy app (scipy signal find peaks)(made for me by Daniel Miller from online resources and libraries) which allowed settings of “prominence” “distance”  “width”   “threshold”  and “height”.  See below. The image of a surfactant protein D dodecamer has been in this blog dozens of times. I used (image processing = either a 5 or 10 px gaussian blur, and on half the images i used an additional filter –  limitrange (100-255)- using Gwyddion. Image processing was applied before signal processing (gaussian blur of 5 px or 10 px, and limitrange. The image processing programs are listed below. The whole dataset comprised 10 dodecamers (thus 20 hexameric arms).

All settings that I used in Octave, AutoFindPeaksPlot were lower than those which I thought should be counted.  Below see my counts of the plots generated by Octave while counting peaks, and the results of counting peaks using various settings in AutoFindPeaksPlot.m (see table, at bottom) You can see from my counts of peaks present on the output plots that accompanied the other values (peak height, width), that the autofindpeaks values (at least the default values, and a few that I typed in) are much less lenient.  I found Ipeaks.m was closer to what I liked, and likely Autofindpeaksplot.m wont be used on the other 100+ images.